SCF format files are used to store data from DNA sequencing
instruments. Each file contains the data for a single reading and
includes: its trace sample points, its called sequence, the positions
of the bases relative to the trace sample points, and numerical
estimates of the accuracy of each base. Comments and "private data"
can also be stored. The format is machine
independent and the first version was described in Dear, S and Staden, R. "A
standard file format for data from DNA sequencing instruments", DNA
Sequence 3, 107-110, (1992).

Since then it has undergone several important changes. The first allowed for
different sample point resolutions. The second, in response to the need to
reduce file sizes for large projects, involved a major reorganisation of the
ordering of the data items in the file and also in the way they are
represented. Note that despite these changes we have retained the original
data structures into which the data is read. Also this reorganisation in
itself has not made the files smaller but it has produced files that are more
effectively compressed using standard programs such as gzip. The io library
included in the package contains routines that can read and write all the
different versions of the format (including reading of compressed files). The
header record was not affected by this change. This documentation covers both
the format of scf files and the data structures that are used by the io
library. Prior to version 3.00 these two things corresponded much more
closely.